One point I should make -- if you play music through your system with only one channel + sub active and tweak THAT to sound correct then you will get exactly the phenomenon you are worried about. That's because you tweaked the system to compensate for the centered bass signal being down 3dB on each channel.
As long as you have all your channels powered up when testing it shouldn't matter whether your test tones are one-speaker or both-speaker because the level will be dropped 3dB for both-speaker.
The big difference IMO is that if you're testing with a tone going to both speakers it's like having two subs to even out your deep bass response -- the warts of one speaker placement can sometimes cancel out the warts of the other speaker placement resulting in a smoother overall response.
Now quit yakking about this and go finish your report
